The major issue with a lot of this work is how you could identify a novel pathogen and know it’s a pathogen. It’s not just about detecting something before it gets recognised as an outbreak, it’s also about that info being actionable—if you don’t know if something is a human pathogen or how it spreads and the only thing to do once an alert is raised is wait to see if clinical cases start showing up in hospitals, it’s not much of an early warning system.
An alternative is to look at airplane waste, since you’ve got a higher probability that whatever you find came from a human, and you have a list of people to track down and see if they have mild symptoms of illness that haven’t reported or asymptomatic infections. You also have info on where the disease has been imported from, which can again give you more info on what to do next.
This is another nice piece of work looking at this problem, where cost of sequencing is factored in and they are working with pooled samples under different strategies: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4164148
The major issue with a lot of this work is how you could identify a novel pathogen and know it’s a pathogen. It’s not just about detecting something before it gets recognised as an outbreak, it’s also about that info being actionable—if you don’t know if something is a human pathogen or how it spreads and the only thing to do once an alert is raised is wait to see if clinical cases start showing up in hospitals, it’s not much of an early warning system.
An alternative is to look at airplane waste, since you’ve got a higher probability that whatever you find came from a human, and you have a list of people to track down and see if they have mild symptoms of illness that haven’t reported or asymptomatic infections. You also have info on where the disease has been imported from, which can again give you more info on what to do next.